Antibody reactivities are traditionally studied by their individual reactivities to one or only a few antigens, whereas only a small number of studies have focused on the repertoires of antibodies to large numbers of defined antigens. Only recently, a new technology for system level analysis, the immune microarrays (or antigen chips) was introduced [Quintana 2004, Quintana and Cohen 2004, Robinson 2006]. This technology is capable of detecting patterns of antibodies binding to many hundreds of antigens, foreign or self and thus allowing a systems biology view of immune system. To create the antigen chips, a robotic apparatus is used to spot the antigen molecules of choice - proteins, peptides, sugars, lipids, nucleic acids - to a coated glass slide. These antigens are covalently linked to the surface of the slide and a drop of blood serum or any other body fluid can be tested for antibodies binding to hundreds of these antigen spots. The subject's bound antibodies are detected using fluorescence-labeled second antibodies and the reactions are monitored by laser activation.